Peter and Caitlin walk through empty streets, as Peter shouts for someone. A truck pulls up, and a CDC hazmat crew climbs out, apprehending the two. Peter calls for Caitlin as they are taken away forcefully.

After being showered and forcefully split, a Homeland Security agent, Howard Lemay, tells Peter that Caitlin will be deported back to Ireland, and hands Peter his death certificate. Peter asks what is happening, and Howard shows him around the CDC building. He says that the Shanti virus wiped out 93% of the world's population, and then shows him a room filled with body bags.

Howard takes Peter to see the future version of his mother who the CDC has brought in to try to restore Peter's memory. Angela describes who Peter is and explains that nature of his ability. Angela tells Peter that he possesses the ability to travel in time due to meeting Hiro Nakamura and he must remember so he can return to his own time period and change history. When Peter insists he can't remember, Angela tells him that if he doesn't alter history, the virus will kill everyone. Peter is able to learn who Angela is to him through reading her mind and the two embrace.

As Angela leads Peter to their home, Caitlin calls for Peter in a deportation line. They grab hold of each other as best they can and Peter attempts to return them to their own time period. Caitlin is dragged away before Peter can succeed and he inadvertently returns to his own time alone.

As Peter tells Adam Monroe about the future he witnessed, he experiences a vision where he witnesses himself and Caitlin be dragged away by the CDC hazmat crew. Peter awakens to a confused Adam and they discover he has brought back an evacuation notice from the future with him. Adam questions Peter on what he knows of the virus and Peter tells him he knows it kills 93 percent of the world's population within a year and that Howard Lemay told him it was called the Shanti virus while he was in the future. Adam shows Peter a picture of the Company founders and tells him that one, Victoria Pratt, extracted a deadly virus from a young Indian girl named Shanti on February 14, 1977 and on Company orders began manipulating the virus into a weapon. Adam claims he heard the virus program was shut down but was apparently misinformed. Peter realizes that the Company is responsible for the release of the virus and they need to find Victoria so she can tell them where to look.

After finding out the date that Adam was locked up by his father, Hiro travels back in time to November 2, 1977 where he witnesses Adam captured. Adam tells Kaito that with all the wars and famine humans are causing across the world, the only way to save it is to release a virus that will cause billions of people to die. Hiro watches as Victoria tells Kaito that Adam was after Strain 138, a strain that would've caused a global pandemic if it had been released. Kaito refuses to destroy the virus and instead orders it locked up in the Primatech facility in Odessa, Texas, believing it will be safe there with Adam locked away. Victoria refuses to have anything more to do with the Company as a result and Hiro returns to the present where he tells Ando that Adam is trying once more to release the virus and he has to stop him.

In Searsmont, Maine, Peter finds Victoria's home and tells her that in 24 hours, the Shanti virus will be released and within a year over 93% of the world's population will be dead. When Victoria questions his knowledge of this, Peter admits he's visited the future that results and he doesn't know how or where the virus will be released, just that it will be. Victoria leads Peter into her house and is skeptical about his motives as she only knew his parents. Peter tells Victoria that he left Caitlin behind in the future and can't return to her but believes if he can find the virus, he can save her. Victoria finally tells Peter that he's looking for Strain 138 of the virus and if it were ever to get out, it would kill all human life on the planet. Victoria lies to Peter about the location of the virus, but is captured by him when she tries to kill Adam. Victoria tells Peter that Adam had tried to release Strain 138 before and she'd stopped him and now he's doing it again. Peter insists that they are only trying to find Strain 138 so that he can destroy it and change the future and eventually reads her mind to find out where the virus is. After killing Victoria, Adam tells her body that if anyone survives the virus, he'll tell them he couldn't have done it without her.

On March 20, 2007, Peter and Adam enter Primatech Paper to destroy Strain 138 of the Shanti virus and stop its release and thus the outbreak future. Hiro appears to kill Adam in revenge for Adam murderinghis father. During the confrontation that follows, Peter tells Hiro about the future he saw and that it starts at Primatech that day unless they destroy the virus. Peter then uses the opportunity to stun Hiro.

After Peter and Adam reach the Primatech vault, Peter questions Adam on Kaito's murder. While Adam admits to the murder, he tells Peter that Kaito had the virus locked up instead of destroyed so he could use it in the future. When Peter hesitates, Adam reminds him that Caitlin is trapped in a future where nearly everyone's dead from the virus and Caitlin and the world needs Peter to open the door so they can destroy the virus. Peter reluctantly starts using telekinesis to pry open the vault door to get at the virus.

After Nathan convinces him that Adam is manipulating him, Peter gets into the vault just in time to catch the virus with telekinesis and stop it from being released. Peter is horrified as he'd seen the outbreak future and what would've happened if the virus was released and he nearly caused its release. After being reminded by Nathan that he'd come to destroy the virus, Peter cups it in his hands and destroys the virus with a blast of radiation, averting the outbreak future.

In the original ending of Powerless, Adam succeeds in dropping the vial and releasing the virus. However, the Writer's Strike resulted in this and many other scenes being deleted. They are featured on the season two DVD.

The virus escapes through the vents of Primatech infecting a nightshift worker, a forklift operator, and other Primatech employees and the surrounding citizens. Peter, Nathan and Matt rush down to the ground floor towards a way out when they see that the workers have fallen unconscious due to the infecting virus. Peter, Nathan, and Matt then agree that they must quarantine the whole town so they go to the police. Officer White will not listen to them and so they take matters into their own hands. Matt uses his powers to get everyone in the police station to listen to Nathan. Nathan instructs them that they must set up this blockade around the town. A conceptual storyboard scene is then shown where Peter telekinetically causes a landslide to block the only bridge in or out of town. After the scene when Sylar escapes from Mohinder's loft that is used in the actual episode Powerless, reporter Bruce Evans wants Nathan (the leader of this operation) to go public with this news to let everyone know what is happening. When reporting on front of an audience, Nathan faints. The virus has affected him.

In a Season Two DVD commentary, it is explained that originally, Odessa, TX was quarantined. Eventually, it would be learned that Howard Lemay was an agent of the Company, who used his position at the CDC to quarantine Odessa to ensure that the Company's existence was kept secret. He was intended to be the main villain of the originally planned Volume 3, Exodus.